The main characters might interact with historical superheroes or villains that no longer exist in their present time. For instance, they could meet an ancient sorcerer - villain who was sealed away long ago. Dealing with such a character would test their skills and force them to think outside the box in terms of combat and strategy.
The main characters would most likely be the core members of the Young Justice team, like Robin, Superboy, and Miss Martian. They are the central figures in the original Young Justice series, so it's natural for them to be the main characters in this fanfiction as well.
Obviously, the main characters from Young Justice like Robin, Aqualad, and Kid Flash would be there. They are the core of the group and their personalities would create a lot of interesting situations in high school.
Obviously, the young justice members themselves will be there. And then, of course, Batman is very likely to show up. He is Gotham's main protector after all.
Obviously, the members of the Justice League like Superman, Batman, Wonder Woman, The Flash, Green Lantern etc. would be main characters. And in Gotham, we can't forget the villains such as the Joker, Penguin, and Catwoman. They are likely to play important roles as well.
Obviously Naruto himself. Since he is the one going to the past, he would be the central character. His younger self would also be important as he would interact with his future self.
Family members or friends of the Young Justice members could be main characters too. They would be dealing with the grief and might be involved in trying to find out the truth or get justice. Their emotional journey could be a big part of the story, and they could interact with the other characters in different ways, like pushing the heroes to act or providing support in unexpected ways.
The main character is Naruto. In the past, he will surely encounter his parents. Minato and Kushina would be important characters in this fanfic. Also, Jiraiya, his mentor, would be a key figure. Since Naruto is going to the past, he might seek Jiraiya's guidance even more. And characters like Orochimaru would also be part of the story as Naruto may try to stop Orochimaru's evil plans earlier.
Robin is often one of the main characters to interact with Kakashi. Since Robin is a brilliant strategist, he and Kakashi can have some really interesting exchanges about tactics and planning.
Probably Naruto and Robin. Robin is the leader - type in Young Justice, always thinking and strategizing. When Naruto shows up, Robin would be the one to approach him first, trying to figure out who he is and what his intentions are. Naruto, being friendly and curious, would be open to the interaction.
Simon, if he makes an appearance in the fanfiction, would have a very different dynamic with Marceline. He has a long history with her and his wisdom could play a crucial role in helping her understand and manage her 'vampire in heat' situation. His presence could also bring up a lot of memories for Marceline, which would add depth to the story.